Shulou(Shulou.com)06/01 Report--

In this issue, the editor will bring you how to understand the circular RNA annotation tool circAnno. The article is rich in content and analyzes and narrates it from a professional point of view. I hope you can get something after reading this article.

When using RNA_seq data to predict circular RNA, in most cases, we can only get the genome position of circular RNA, including head and tail chromosome position, positive and negative strands and other information, but there is no corresponding source gene, sequence and other information of circular RNA. These information need to be compared with the existing linear RNA data, which is called circular RNA annotation in the analysis.

For circular RNA annotation, different teams have different approaches. The core is to compare the genomic location of circular RNA with known transcripts to determine whether there is overlap with known transcripts, so as to determine the source genes and corresponding transcripts.

In the starBase database, a series of annular RNA annotation tools are provided

CircSeeker and circAnno are the tools used to annotate ring RNA.

CircAnno needs two input files, one is the bed format file corresponding to the ring RNA, and the other is the bed12 format file corresponding to the linear RNA. Take the ring RNA in the circBase database as an example to see the specific usage of this software.

1. Download the ring RNA data wget http://www.circbase.org/download/hsa_hg19_circRNA.bedcut-F1-6 hsa_hg19_circRNA.bed > circRNA.bed62 from circBase. Download refseq transcript data from UCSC

Download using table browser, as shown below

3. Run comment circAnno hg19.bed12.txt circRNA.bed6 > annotation.xls

The output is as follows

The contents of the first six columns are the contents of the bed file of the annular RNA, but the transcript comment information is added to the fourth column. The match indicates an exact match with the transcript's exon, overlap indicates overlap, and intergenic represents the intergenic region. The last three columns represent the number of exons, the length of exons and the starting position of exons in the overlapping region, which are consistent with those in the bed12 file.

This is how the annular RNA annotation tool circAnno shared by the editor is understood. If you happen to have similar doubts, you might as well refer to the above analysis to understand. If you want to know more about it, you are welcome to follow the industry information channel.

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